simple_fluor_FLUCT_light_curve_with_recovery


goes with simple_fluor_light_curve_with_recovery
/**
 * Macro for data evaluation on PhotosynQ.org
 * by: David M. Kramer
 * created: September 13, 2018 1:43 PM
 */

// Define the output object here
var output = {}; 
  
// Check if the key time exists in json 
if (json.time !== undefined){
    // Add key time and value to output
    output.time = json.time;
}

// define the points in each sub-trace to use for calcualtions of Fv/FM or Fv'/Fm'

var points_to_use_for_F0 = [0,6];  // For F0 or Fs, we will take the minimum value of the sub-trace points from 0 to 6 
var points_to_use_for_FM = [100,200];  // For Fm anf Fm', we will use the maximum value of the points from 100 to 200 
var fraction_light_to_PSII = 0.45;
    
var PAR = json.v_arrays[0]; // PAR is defined in the first array of json.v_arrays

var repeats_at_each_light = json.v_arrays[1][1]; // the number of repeats o	f the Fv/Fmp traces at each light
    
output.PAR=PAR;  // send the PAR data to the output.

var fTraces=[];  // array to contain the fluorescence traces
var Fs=[];  // array to contain the Fs values
var FMp=[];  // array to contain the Fm' values
var Phi2=[];  // array to contain the calculated Phi2 values
var LEF = [];  // array to contain the calculated LEF values
var NPQ=[];  // array to contain the calculated NPQ values

ftrans=GetProtocolByLabel( "ftrans", json, true );  // the GetProtocolByLabel command will return an array of 
											  // all data_raw traces labelled as "ftrans". We will have MathEXPINVREG(values)	
											  // a series of these, the total number = (number of light settings) * number of 
											  // protocol_repeats at each.

// find Fs, FMNp values and calculate Phi2

var number_cycles =  ftrans.length / repeats_at_each_light;
output.number_cycles = number_cycles;

var iii=0;
for (var i=0; i<number_cycles; i++){  //cycle through the light intensities
  for (var ii=0; ii<repeats_at_each_light; ii++) {  //cycle through the repeats at each light
    
   var Fst = MathMIN(ftrans[iii].data_raw.slice(points_to_use_for_F0[0],points_to_use_for_F0[1])); 
    					// For F0 or Fs, we will take the minimum value of the sub-trace points 
    					// from points_to_use_for_F0[0] tp points_to_use_for_F0[1]
    
   Fs.push(Fst);     // add the value to the array 
   var FMpt = MathMAX(ftrans[iii].data_raw.slice(points_to_use_for_FM[0],points_to_use_for_FM[1]));
    					// For Fm or Fmp, we will take the MAXIMUM  value of the sub-trace points 
    					// from points_to_use_for_FM[0] tp points_to_use_for_FM[1]

    FMp.push(FMpt);  // add the value to the array 
   var Phi2t=(FMpt-Fst)/FMpt;   // calculate Phi2 
   Phi2.push(Phi2t);    // add the value to the array 
   LEF.push(fraction_light_to_PSII * Phi2t * PAR[i]);  // calculate LEF as PAR * fraction_light_to_PSII * Phi2
    									               // and add the value to the array 
    iii++;
  }
} 

FM=FMp[0];  // set the first Fmp value as Fm
output.FM = FM;

for (var i=0; i<ftrans.length; i++){
	NPQ.push((FM-FMp[i])/FMp[i]);	
}

output.Fs=Fs;
output.FMp=FMp;
output.Phi2=Phi2;
output.NPQ=NPQ;
output.LEF=LEF;
return output;
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  "device_name": "MultispeQ",
  "device_version": "2",
  "device_id": "32:21:3c:e5",
  "device_battery": 106,
  "device_firmware": 2.0038,
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Dave in cap img 4615
Created by

David M. Kramer


Protocol connections:
0
Latest Update:
Dec 2018